Image Formats

EVAnalyzer reads images through the open-source Bio-Formats library, which is bundled with the application. Both 8-bit and 16-bit greyscale and 8-bit RGB colour images are supported.

Supported Extensions

tif  tiff  btif  btiff  btf
jpg  jpeg
vsi  ics  czi  nd2  lif  lei
fli  scn  sxm  lim  oir  top
stk  nd  bip  msr  dm3  dm4
img  cr2  ch5  dib  ims  pic
raw  1sc  std  spc  avi  cif
sif  aim  svs  arf  sld  ome.tiff

A complete list of all Bio-Formats–supported formats is available at docs.openmicroscopy.org.

Best results

Use raw, uncompressed images directly from your microscope without any pre-processing or compression applied. For multi-channel images, keep the channels in their original multi-channel format rather than merging them into an RGB image.

Caution

Certain Photoshop-encoded TIFF files are not supported. Use RAW TIFF or OME-TIFF for multi-channel TIFF files.

Image Planes {#image-planes}

A single microscopy file typically contains many individual images organised into three dimensions:

Dimension	Symbol	Description
Channel	C	Fluorescence or brightfield channel
Z-plane	Z	Focal plane in a z-stack
Time frame	T	Frame in a time-lapse sequence

Each unique combination of (C, Z, T) is one image plane. EVAnalyzer can access and process any plane individually.

Pipeline input is specified by channel index (0-based). Z and T handling is configured in the Project tab.

OME-XML Metadata {#ome-xml}

EVAnalyzer reads OME-XML metadata embedded in or alongside image files. OME metadata provides:

• Number and order of channels
• Physical pixel sizes (nm/µm/mm)
• Z-step size

Caution

If no OME metadata is found in a multi-channel file, EVAnalyzer assumes a single channel. Ensure your multi-channel images include valid OME metadata for correct channel loading.

Big Images {#big-images}

Large whole-slide images are handled automatically via tiling. EVAnalyzer splits any image larger than the configured tile size into overlapping tiles, analyses them independently, and stitches the results.

The maximum tile size (default: 4096 × 4096 px) is set in the Project tab. A smaller tile size reduces RAM usage at the cost of more tile transitions.

Note

EVAnalyzer can generate a navigator minimap for big images only when the file contains a pyramid representation (reduced-resolution levels). Ensure pyramid support is enabled when saving whole-slide images.

Formats that support big (pyramid) images:

.afi  .svs  .ims  .vsi  .ndpi  .ndpis  .jp2
.tiff .tif  .tf2  .tf8  .btf   .sld    .jpg  .czi

The hard image-size limit is 46 340 × 46 340 pixels (the 32-bit signed integer limit used by many image-processing algorithms).